Contacts of the helix formed by residues 42 - 56 (chain D) in PDB entry 1PY1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 42 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D ASP* 2.6 33.7 - - - +
41D PHE* 1.3 106.2 - - + +
43D GLY* 1.3 62.2 + - - +
44D PRO 3.5 2.0 - - - -
45D PRO* 3.3 20.0 - - + +
46D LEU* 3.5 18.2 + - + +
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Residues in contact with GLY 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LEU* 3.6 13.4 - - - +
36D GLN 5.7 0.2 - - - -
37D LEU 3.4 13.0 - - - -
40D ASP* 3.8 14.2 - - - +
41D PHE 3.5 0.4 - - - -
42D GLU* 1.3 80.0 + - - +
44D PRO* 1.3 65.3 - - - +
46D LEU* 3.1 7.5 + - - +
47D ALA* 2.7 30.5 + - - +
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Residues in contact with PRO 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 3.2 31.4 - - + +
40D ASP 4.2 6.1 - - - +
41D PHE 4.1 9.0 - - - +
42D GLU 3.7 0.4 - - - -
43D GLY* 1.3 87.0 - - - +
45D PRO* 1.3 72.2 - - + +
47D ALA* 3.0 13.4 + - + +
48D THR* 3.0 16.5 + - - +
80D ARG* 3.7 38.6 - - + +
81D PHE* 4.7 2.2 - - + -
84D GLU* 3.6 20.0 - - + -
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Residues in contact with PRO 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D PHE 4.7 2.0 - - - +
42D GLU* 3.3 23.6 - - + +
44D PRO* 1.3 99.2 - - + +
46D LEU* 1.3 57.4 + - - +
48D THR* 3.1 14.5 + - - +
49D ARG* 3.3 20.5 - - - +
84D GLU* 3.5 32.5 - - + +
89D ARG* 6.5 0.7 - - - -
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LEU* 3.9 23.6 - - + -
11D GLU* 3.9 19.7 - - - +
42D GLU* 3.5 16.8 + - + +
43D GLY* 3.1 8.5 + - - +
44D PRO 3.1 0.8 - - - -
45D PRO* 1.3 77.3 - - - +
47D ALA* 1.3 61.2 + - - +
49D ARG* 3.3 28.5 + - - +
50D LEU* 3.0 47.9 + - + +
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Residues in contact with ALA 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LEU* 4.0 4.0 - - + -
33D PHE* 3.5 29.8 - - + -
37D LEU* 3.7 24.0 - - + -
43D GLY 2.7 20.1 + - - +
44D PRO* 3.6 4.9 - - + +
46D LEU* 1.3 75.6 - - - +
48D THR* 1.3 62.9 + - - +
50D LEU* 3.5 2.1 + - - +
51D LEU* 3.1 30.1 + - - +
81D PHE* 4.4 5.4 - - + -
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Residues in contact with THR 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D PRO 3.0 5.7 + - - +
45D PRO* 3.1 18.2 + - - +
47D ALA* 1.3 76.0 - - - +
49D ARG* 1.3 57.5 + - - +
51D LEU* 3.5 3.9 + - - -
52D ALA* 2.9 24.8 + - - +
81D PHE* 3.8 19.3 - - + -
84D GLU* 3.5 40.8 + - + -
85D VAL* 4.2 7.4 - - + +
89D ARG* 6.1 0.9 - - - +
90D PHE* 3.3 36.4 - - + +
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Residues in contact with ARG 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C PRO* 3.9 36.5 + - + +
106C ARG* 4.2 50.0 + - - +
45D PRO 3.3 17.5 - - - +
46D LEU* 3.3 28.7 + - + +
47D ALA 3.2 0.4 - - - -
48D THR* 1.3 79.9 + - - +
50D LEU* 1.3 66.6 + - + +
52D ALA* 3.3 5.8 + - - +
53D HIS* 3.2 22.2 + - - +
89D ARG* 6.2 5.8 - - + +
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Residues in contact with LEU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C PRO* 4.1 25.6 - - + -
59C GLN* 4.2 14.6 - - + +
10D LEU* 4.1 8.7 - - + -
11D GLU* 3.8 45.1 - - + +
14D ILE* 4.5 17.7 - - + -
33D PHE* 4.7 5.2 - - + -
46D LEU* 3.0 42.3 + - + +
47D ALA* 3.9 4.3 - - - +
49D ARG* 1.3 76.4 - - - +
51D LEU* 1.3 57.9 + - - +
53D HIS* 3.4 3.8 + - - +
54D LYS* 3.1 32.0 + - + +
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Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ILE* 3.7 11.9 - - + -
33D PHE* 4.2 17.0 - - + -
47D ALA 3.1 21.6 + - - +
48D THR* 3.7 6.7 - - - +
50D LEU* 1.3 75.2 - - - +
52D ALA* 1.3 55.9 + - - +
53D HIS 3.1 1.6 - - - -
54D LYS* 3.1 4.0 + - - +
55D ILE* 2.7 48.3 + - + +
66D ALA* 3.5 30.1 - - + +
69D VAL* 3.5 20.9 - - + +
70D LEU* 4.4 16.8 - - + +
81D PHE* 3.9 28.5 - - + -
90D PHE* 4.5 2.5 - - + -
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Residues in contact with ALA 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D THR 2.9 19.1 + - - +
49D ARG* 3.9 5.8 - - - +
51D LEU* 1.3 75.4 - - - +
53D HIS* 1.3 60.4 + - - +
55D ILE* 3.5 5.7 + - - +
56D GLN* 2.9 35.7 + - - +
90D PHE* 4.0 12.3 - - + -
93D GLU* 3.6 36.3 - - + -
94D LEU* 6.4 0.4 - - - -
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Residues in contact with HIS 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C HIS* 2.8 80.6 + + - -
54C LYS* 5.1 0.7 - - + -
56C GLN* 3.9 9.6 - - + -
57C SER* 3.3 34.2 - - - -
58C PRO* 3.5 24.0 - - + +
59C GLN* 5.8 1.0 + - - -
62C GLU* 3.8 9.1 + - - -
49D ARG 3.2 9.0 + - - +
50D LEU 3.7 7.2 + - - +
51D LEU 3.1 0.4 - - - -
52D ALA* 1.3 79.5 - - - +
54D LYS* 1.3 75.7 + - - +
56D GLN* 3.3 16.6 + - - +
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Residues in contact with LYS 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C HIS* 4.8 0.8 - - - -
54C LYS* 5.8 1.2 - - - +
59C GLN* 4.0 10.8 - - - +
62C GLU* 4.0 18.6 + - - -
14D ILE* 4.4 11.7 - - + -
15D ASN* 3.2 32.2 + - - +
18D THR* 3.3 32.1 - - + +
50D LEU* 3.1 19.7 + - + +
51D LEU* 3.6 4.5 - - - +
53D HIS* 1.3 90.2 + - + +
55D ILE* 1.3 61.0 + - - +
57D SER* 3.2 22.0 - - - -
62D GLU* 3.4 25.3 + - + +
63D ALA* 3.3 11.6 + - - -
66D ALA* 3.6 15.0 - - + -
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Residues in contact with ILE 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LEU* 2.7 42.8 + - + +
52D ALA* 3.9 7.0 - - - +
54D LYS* 1.3 72.9 - - - +
56D GLN* 1.3 57.5 + - + +
57D SER 3.2 1.6 + - - +
63D ALA* 3.2 22.1 - - - +
66D ALA* 3.8 17.5 - - + +
67D LEU* 3.6 38.8 - - + -
70D LEU* 3.9 17.7 - - + -
90D PHE* 4.3 9.2 - - + -
94D LEU* 4.3 10.3 - - + -
97D VAL* 4.4 10.1 - - + +
107D THR* 5.9 0.2 - - - +
111D VAL* 4.4 7.0 - - + +
115D ILE* 3.9 19.3 - - + -
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Residues in contact with GLN 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C HIS* 3.7 11.0 - - + -
52D ALA* 2.9 22.0 + - - +
53D HIS* 3.3 12.0 + - - +
55D ILE* 1.3 76.9 - - + +
57D SER* 1.3 64.5 + - - +
58D PRO* 3.5 3.8 - - - +
93D GLU* 2.7 52.8 + - - +
96D LYS* 4.7 7.5 - - - +
97D VAL* 3.5 23.2 - - + +
103D LEU* 4.3 21.1 - - + +
107D THR* 6.1 0.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il